Biology subjects

Ye, K.

Publications and source records attributed to Ye, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Cellular context shapes the transcriptomic impact of somatic variants

Somatic SNVs are commonly prioritized by recurrence or sequence annotation, leaving the molecular consequences of private variants unresolved. We developed PrismSNV and Ligo-Seq, a single-cell full-length transcriptome sequencing platform, to quantify transcriptomic displacement associated with within-cell SNV-state toggling. Across 26 samples from three cancer types, more than 60% of candidate SNVs showed significant cell-type-specific displacement with over 30% variation in magnitude. Sequence-based deleteriousness was poorly aligned with cellular displacement, and fewer than 3% of top-displacement SNVs across six tumor types were catalogued in ClinVar. Displacement was strongest in transcriptionally plastic, less differentiated states. Analysis of 655,349 CD4+ T-cell transcriptomes further showed that SNV-gene associations changed in magnitude and sometimes direction during activation. Lack of recurrence or clinical annotation does not imply transcriptomic inertness; variant impact is shaped by cellular context rather than sequence alone, establishing the variant-cell pair as a critical unit for interpreting somatic variation.

genetics↗

bioRxiv2026

Structure of influenza D virus NS1 reveals a novel Zn-binding site and ssRNA-binding activity

Influenza D virus (IDV) is an emerging pathogen associated with bovine respiratory disease and has potential for zoonotic transmission. Although nonstructural protein 1 (NS1) is a major virulence factor in influenza A and B viruses, the structure and function of IDV NS1 remain poorly defined. Here, we determined crystal structures of the IDV NS1 N-terminal RNA-binding domain (NTD) and C-terminal effector domain (CTD). The NTD retains the conserved homodimeric six-helix fold, whereas the CTD adopts a distinct architecture containing a novel Zn2+-binding site. IDV NS1 CTD preferentially binds single-stranded RNA, and mutagenesis identified lysine and arginine residues critical for this activity. Single-residue substitutions disrupting either the Zn2+-binding site or RNA-binding interface prevented recovery of infectious recombinant IDV. These findings reveal distinct structural and functional features of IDV NS1 and establish the importance of CTD integrity for viral replication. Conservation of key CTD residues in influenza C virus NS1 suggests shared structural features that distinguish influenza C and D virus NS1 proteins from their influenza A and B counterparts.

biochemistry↗

bioRxiv2026

Chimeric archaeal BHB-human pre-tRNA scaffold HARBOR system enables versatile production of functional circular RNA modalities

Circular RNAs (circRNAs) exhibit superior intrinsic stability and lower immunogenicity compared with linear RNAs, rendering them promising modalities for biomedical and biotechnological applications. Here, we establish the HARBOR (Human-Archaeal RNA Backbone for Overexpression of circular RNA) system, an engineered endogenous circRNA expression platform integrating a human precursor transfer RNA (pre-tRNA) scaffold with an archaeal Bulge-Helix-Bulge (BHB) motif. HARBOR repurposes the endogenous tRNA splicing machinery to generate chimeric pre-tRNA intermediates, which are rapidly degraded following processing, while producing circRNAs ranging from hundreds of nucleotides to 8 knt in cells and in vivo. Notably, it enables robust production of large-sized circRNAs with yields nearly 80-fold than the intronic complementary sequence-mediated back-splicing (3D5) system and can drive protein expression from translatable circRNAs at an efficiency close to 20-fold than the Tornado system. Such prominent properties support diverse applications of HARBOR, including producing therapeutic aptamers targeting PKR-associated neuroinflammation and pathological TDP-43 condensation, as well as protein-coding circRNAs encoding adenine base editors for genome editing and MYOD1 for fibroblast-to-myocyte trans-differentiation. Collectively, HARBOR represents a versatile, scalable, and user-friendly platform that unifies circRNA-based aptamer and protein expression applications, advancing circRNA-enabled engineering and biomedical applications.

molecular biology↗

bioRxiv2026

Ultra-fast and scalable high-resolution full-length single-cell RNA sequencing using CHART-seq

Plate-based full-length single-cell RNA sequencing resolves transcript structure details but remains difficult to scale because each cell usually requires a separate library. Here we developed CHART-seq (Combinatorial Heteroduplex Assay via Recombinant Tn5), which uses orthogonally indexed Tn5 complexes to tagment RNA/cDNA heteroduplexes and permits early sample pooling. The workflow processed up to 96 cells per library, was compatible with 384-well expansion, and completed library preparation within 3 h at a reagent cost below US$1 per cell. At matched sequencing depth, CHART-seq detected more genes and annotated isoforms than Smart-seq2, Smart-seq3, Flash-seq and SHERRY2, while retaining broad genebody coverage and reproducible expression estimates. In the CHART-seq results of vascular smooth muscle cells, TGF-{beta}1 pretreatment before PDGF-BB exposure partly restored contractile features, suppressed a PDGF-associated inflammatory programme, and induced a distinct metabolic-matrix response with coordinated transcript-usage changes. These biological findings remain exploratory because independent biological replicates were unavailable. CHART-seq provides a rapid, scalable route to full-length single-cell transcript profiling with gene-programme and candidate isoform resolution.

genomics↗

bioRxiv2026

Benchmarking Twist Genotyping-by-Sequencing Against Whole-Genome Sequencing in Nuclear Families

Genome-wide genotyping is widely used in human genetics research, and targeted sequencing-based approaches such as the Twist Bioscience genome-wide SNP capture platform (GxS) have emerged as alternatives to conventional SNP arrays. Here, we evaluated GxS genotype calls from 555 individuals in 184 nuclear families against matched whole-genome sequencing (WGS) calls and compared platform performance with that of the Illumina Infinium Global Screening Array-24 (GSA), which was evaluated in 987 individuals from 279 nuclear families. Genotype data were harmonized across platforms, and analyses were restricted to overlapping SNP loci. Across all callable positions, mean per-SNP call rates were 98.26% for GxS and 98.67% for GSA. Overall SNP concordance with WGS was 99.79% for GxS and 99.87% for GSA, and mean per-individual concordance was also 99.79% and 99.87%, respectively. Per-trio Mendelian violation rates of GxS are about 10 times those of WGS, while those of GSA are about 4 times those of WGS on average. These results indicate that GxS performs slightly worse than GSA by key concordance and inheritance metrics, while still showing strong overall agreement with WGS.

bioinformatics↗

bioRxiv2026

Multidimensional variation and population stratification across 8000 complete human centromeres

Human centromeres are indispensable for the faithful segregation of chromosomes during cell division, yet their highly repetitive nature has historically precluded comprehensive characterization, leaving fundamental questions about their sequence diversity, evolution trajectories and function dynamics unresolved. Here, we generated 6,312 complete human centromere sequences from 320 phased genome assemblies in Asian Pan-Genome project phase 1. By integrating the assemblies from the Human Pangenome Reference Consortium (HPRC) and Human Genome Structural Variation Consortium (HGSVC), we constructed a multidimensional genetic variation map encompassing over 8,000 gapless centromeres. Centromeric satellite arrays account for 4.19% to 6.01% of the whole genome, with substantial variations in size and architecture across chromosomes. Using a refined alpha satellite clustering approach that captures global diversity, we identified 195 higher-order repeat (HOR) arrays, 56.4% of which are absent from the T2T-CHM13 reference genome. Extensive structural variations across multiple dimensions exhibit population stratification, including centromeric haplotypes (CenHaps), ultra-large pericentric inversions spanning up to 36.6 Mbp, and inter-chromosomal HOR sharing that reflects sequence exchange among chromosomes. Integrating CENP-A CUT&Tag experiments and long-read-based DNA methylation profiles, we demonstrate that 16.8% of centromeres harbor multiple potential kinetochore assembly sites, and CenHap-specific local HOR homogenization is associated with kinetochore positioning. Despite global suppression of recombination at centromeres, we observed asymmetric linkage disequilibrium flanking centromeres and an ancient recombination event within the centromere of chromosome 19. Furthermore, contrary to the prevailing assumption of high mutation rates in centromeres, our estimates based on stringent orthology reveal no significantly higher single-base substitution rates for centromeres relative to flanking pericentromeric regions with substantial variations across chromosomes, despite extraordinary structural plasticity. Collectively, these multi-scale centromeric variations provide a global view of human centromere diversity and population stratification, fundamentally redefine centromere evolution through a dual-track model balancing structural innovation with mutational constraint, and establish an essential resource for investigating centromere biology and a baseline reference for diagnosing centromere-associated disorders.

genomics↗

bioRxiv2026

Assembly of a high-quality reference genome for the rat tapeworm Hymenolepis diminuta

The rat tapeworm, Hymenolepis diminuta, is an important laboratory model for uncovering molecular processes that underly the success of tapeworms as parasites. Despite its importance, a high-quality reference genome for this species is lacking. Here we present a highly contiguous and effectively complete genome of H. diminuta assembled from PacBio HiFi long-read sequencing data. Our primary assembly consists of 7 scaffolds (N50=29.25 Mb) with total length of 186.53 Mb, has only 7 gaps, and contains 95.7% complete Lophotrochozoan BUSCOs. Our assembly allows us to confirm aspects of Hymenolepis genome organization, such as high repeat content and unusual chromosomal ends, and to show that Hymenolepis genomes encode [~]10,000 genes. Together with annotations of nuclear tRNAs, mtDNA protein coding genes, and mtDNA tRNAs, our assembly currently provides one of the most complete genome resources for a tapeworm species and will enable research on parasitism, animal regeneration, development, and evolution.

genomics↗

bioRxiv2026

Hunger modulates behavioral responses to olfactory and chemotactile cues in the specialist predator of dangerous prey, Berghia stephanieae

Animals continuously evaluate environmental cues to guide approach-avoidance decisions, with internal states like hunger dynamically shaping how stimuli are acted upon. While most studies examine the valence-switching of stimuli from appetitive to aversive using simplified or ambiguous stimuli, we leveraged a system in which a single prey contains both appetitive and aversive features. The nudibranch Berghia stephanieae, is a specialist predator of the sea anemone, Exaiptasia diaphana. These nudibranchs must resolve conflicting signals where chemical cues signal food, while contact can result in injury or death. The danger posed by Exaiptasia was described and quantified through direct counts of nematocysts fired into Berghia and multiple instances where the Berghia was captured and consumed by its prey. To test how internal state influenced the perception of stimuli from prey we recorded predatory behavior of Berghia after different periods of food deprivation. We found that the olfactory cues from prey were attractive to Berghia, even when animals were sated, and usually led to a contact-mediated investigation of prey. Hunger independently modulated olfactory and contact cue valence at different internal states and time scales of food deprivation. Hunger specifically altered the threshold for avoidance following contact with prey, indicating that somatosensory and chemotactile cues are modulated by hunger unlike olfactory cues. Our results highlight how internal state and sensory modality interact to shape decision making in a biologically relevant, high-risk predation context.

animal behavior and cognition↗

bioRxiv2026

Complete Telomere-to-Telomere Assembly of the Y Chromosome in the Chinese Quartet

The complete assembly of the human Y chromosome remains a formidable task due to its highly repetitive, palindromic, and heterochromatic architecture. While complete telomere-to-telomere (T2T) assemblies have recently been generated for select individuals, high-quality, gapless Y chromosome references for East Asian lineages--specifically within well-characterized multi-omics reference cohorts--remain scarce. The Chinese Quartet (CQ), comprising monozygotic twin daughters and their parents, represents a premier national reference material system for genomic standardization. However, because the female offspring inherited their father's X chromosome rather than his Y chromosome, previous pedigree-based T2T assemblies (CQ v3.2) lacked a gapless Y chromosome sequence. Here, we present a complete, gapless T2T assembly of the Y chromosome (designated CQ_chrY) from the father of the CQ. This assembly was generated by integrating Oxford Nanopore Technologies ultra-long reads, PacBio high-fidelity reads, and Hi-C data, resulting in a sequence of 68.50 Mb. The assembly shows exceptional base accuracy (QV = 57.54) and structural assembly quality (CRAQ AQI = 99.781). We completely resolved the 40.09 Mb Yq12 heterochromatic region, a ~940 kb centromeric higher-order repeat array, and annotated 96 protein-coding gene models evaluated against GENCODE/T2T-Y standards, alongside 57.59 Mb (84.07%) of repetitive elements. CQ_chrY serves as a complementary paternal resource extending the CQ reference platform, providing a robust foundation for population genetics, structural variation analysis, and East Asian genomic standardization.

genomics↗

bioRxiv2026

MEIsensor: a deep-learning method for mobile element insertion discovery

Mobile element insertions (MEIs) are a critical source of structural variation in the human genome, yet their accurate detection remains challenging, particularly within repetitive regions and for structurally complex insertions. While long-read sequencing enables the direct recovery of inserted sequences, current analytical pipelines rely heavily on repeat-library alignment, which can limit both computational efficiency and accuracy. Here, we present MEIsensor, a deep learning framework designed to detect and classify MEIs directly from long-read sequencing data. Unlike conventional methodologies, MEIsensor performs direct, sequence-based annotation of Alu, LINE1, and SVA insertions. Evaluated against HGSVC benchmarks using HiFi long-read datasets, MEIsensor consistently outperformed existing tools across major MEI classes while substantially improving computational efficiency, demonstrating particularly pronounced gains for structurally complex SVA insertions. Furthermore, manual curation confirmed that MEIsensor successfully identifies MEIs hidden in highly repetitive genomic regions, including centromeric higher-order repeats, that were previously absent from benchmark datasets. Together, these advancements establish MEIsensor as an efficient framework for MEI analysis that promises to significantly advance our understanding of human genomic architecture and evolution.

bioinformatics↗

bioRxiv2026

Unbiased Single-Cell Transcriptome-Proteome Co-Profiling Reveals Malignant Dormancy and Post-Transcriptional Buffering of CTCs

Leptomeningeal metastasis is driven by rare cerebrospinal fluid circulating tumor cells (CSF-CTCs). However, the mechanisms underlying their adaptation to chemotherapeutic stress remain elusive, primarily because transcriptomics alone poorly predicts functional protein states. Here, we present scMAPS, a single-cell multi-omics method that employs magnetic-assisted partitioning cell lysates to enable unbiased transcriptome-proteome co-profiling without loss-prone physical splitting and precision device. By coupling scMAPS with our custom CLEAP (CTC Label-free Enrichment and Accurate Picking) system, we performed the first deep multi-omics profiling of rare clinical CSF-CTCs before and after localized chemotherapy, detecting an average of 2,547 proteins and 7,821 genes per cell. The integrated CLEAP-scMAPS pipeline reveals a coordinated prioritizing survival over proliferation malignant dormancy phenotype and identified post-transcriptional buffering as the primary driver of treatment resistance. Our platform enables the comprehensive molecular phenotyping of rare clinical specimens, providing a highly versatile framework for decoding complex post-transcriptional regulatory networks.

cell biology↗

bioRxiv2026

Global O-GlcNAcome Identifies O-GlcNAcylated Proteins Regulating Oligodendrocyte Precursor Cells Differentiation

Oligodendrocyte precursor cells (OPCs) differentiate into myelinating oligodendrocytes to form the myelin sheaths essential for neural function, a process frequently compromised during aging and in diseases like multiple sclerosis. However, the regulatory landscape of myelination remains incompletely understood. Here, we perform a comprehensive proteomic analysis of the O-GlcNAcome in postnatal day 0 mouse OPCs, identifying 165 O-GlcNAcylation sites across 118 proteins. These proteins are mostly nuclear and characterized by single-site modifications. Comparative analysis identifies 74 novel sites and 22 proteins uniquely O-GlcNAcylated in OPCs. Molecular docking suggestes that O-GlcNAcylation might act as a dynamic regulator of OPC differentiation. Notably, global O-GlcNAcylation levels increase during the OPC-to-oligodendrocyte transition. By integrating our findings with multiple sclerosis-related transcriptomic and proteomic datasets, we identify candidate proteins linking O-GlcNAc dysregulation to demyelination. Among these, Vimentin (Vim) exhibits a pronounced age-dependent discrepancy between decreased protein levels and elevated mRNA expression during differentiation. We validate Threonine 35 and 63 as key O-GlcNAcylation sites on Vimentin. Functional assays confirm that blocking Vimentin O-GlcNAcylation enhance the OPC differentiation. Collectively, our study establishes the first O-GlcNAc landscape for OPCs and suggests O-GlcNAcylation as a pivotal regulator for OPC differentiation.

neuroscience↗

bioRxiv2026

Neonatal social communication and single genes predict the variability of post-pubertal social behavior in a mouse model of paternal 15q11-13 duplication

Mental illnesses associated with high-risk copy number variations (CNVs) are characterized by incomplete penetrance and variable severity, with their underlying mechanisms remaining inadequately understood. We hypothesized that such phenotypic variability is evident from the neonatal stage and is, at least in part, attributable to individual differences in the expression levels of CNV-encoded genes in the brain. We conducted an analysis of the quantitative and functional structure of neonatal social communication, assessed post-pubertal social interaction, and evaluated the brain expression levels of genes within the same cohort of a mouse model of paternal human 15q11-13 duplication, a high-risk factor variably associated with neurodevelopmental disorders. Subsequently, computational methods were utilized to identify predictive variables for the variability of post-pubertal social interaction. Mice harboring the 15q11-13 duplication exhibited distinctive call sequences characterized by diverse connections, which lacked the incentive value necessary for effective social communication with mother mice. The neonatal call sequences and the expression levels of Magel2, along with, to a lesser extent, Herc2 and Ndn, in the prefrontal cortex of the 15q11-13 duplication model were predictive of post-pubertal social interaction. Our findings demonstrate that variability in post-pubertal social interaction--a dimensional characteristic of neurodevelopmental disorders--can be predicted by the variability of neonatal social communication and is influenced by the expression levels of specific CNV-encoded genes in the prefrontal cortex. This computational approach has the potential to predict the developmental trajectories of various dimensions of mental illness among CNV carriers in humans and to identify CNV-encoded driver genes in preclinical models, thereby providing potential mechanistic bases for the development of gene-based therapeutic strategies.

neuroscience↗

bioRxiv2025

Population-level structural variant characterization from pangenome graph

Population-level structural variant (SV) profiling is crucial in the era of pangenomes. However, identifying SVs from genome assemblies and pangenome graphs remains a significant challenge. Here we present Swave, a sequence-to-image, deep-learning based method that accurately resolves both simple and complex SVs, along with their population characteristics, from assembly-derived pangenome graphs. Swave introduces projection waves to summarize the dotplot images that capture mapping patterns between reference and SV-indicating alleles in pangenome. These images are analyzed by a recurrent neural network to distinguishes true SV signals from background noise introduced by genomic repeats. Swave demonstrates superior performance in both SV type classification and genotyping compared to existing methods. When applied to a healthy cohort (n=334) and a rare-disease cohort (n=574), Swave reveals complex and polymorphic SV patterns across human populations and identifies potentially pathogenic SVs. These advancements will facilitate the creation of comprehensive population-level SV catalogs, deepening our understanding of SVs in genetic diversity and disease associations.

bioinformatics↗

bioRxiv2025

The evolution of high-order genome architecture revealed from 1,000 species

Spatial genome organization plays a crucial regulatory role, but its evolution remains unknown. Leveraging Hi-C data from 1,025 species, we trace the evolutionary trajectories of 3D genome, through two higher-order architectures, global folding (spatial organization of karyotype) and checkerboard (chromatin compartments). Early life forms, including prokaryotes and unicellular eukaryotes, mostly display random configurations. Through the evolution of plants, global folding became the prominent architecture with eudicots and remained dominant. Animals, however, progressively developed stronger checkerboard throughout vertebrate and invertebrate evolution, and even during early embryogenesis, suggesting a conserved gene co-regulation mechanism. In contrast, plants prefer linear gene clusters over checkerboard. Both strategies of gene arrangement reinforce the biological principle structure determines function: divergent evolutionary paths converge on architectural solutions to meet the greater regulatory demands.

evolutionary biology↗

bioRxiv2025

In Vitro Maturation of Bone Marrow-Derived Dendritic Cells via STING Activation for T Cell Priming

Dendritic cells (DCs) are among the most potent antigen-presenting cells, playing a pivotal role in initiating adaptive immune responses. The STING (Stimulator of Interferon Genes) pathway, a key cytosolic DNA-sensing mechanism, has emerged as a powerful modulator of type I interferon production and CD8 T cell activation. In this study, we aimed to generate and functionally mature bone marrow-derived DCs in vitro by optimizing cytokine conditions and incorporating STING pathway stimulation. Immature DCs were differentiated from murine bone marrow using various concentrations of GM-CSF and IL-4, and characterized by the expression of surface markers CD11c, CD80, and MHC-II. Maturation was induced using a STING agonist, followed by co-culture with naive CD8 T cells isolated from mouse spleens via Magnetic Activated Cell Sorting (MACS). STING-activated DCs exhibited enhanced surface marker expression and significantly promoted CD8 T cell proliferation. Our findings demonstrate that combining optimized cytokine-driven differentiation with STING activation significantly improves DC immunogenicity, offering a promising platform for the development of DC-based cancer immunotherapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/659197v2_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@9f2be1org.highwire.dtl.DTLVardef@1f9dbc4org.highwire.dtl.DTLVardef@cb40a5org.highwire.dtl.DTLVardef@14141_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract created using BioRender.com

bioengineering↗

bioRxiv2025

Deciphering complex interactions between LTR retrotransposons and three Papaver species using LTR_Stream

Long terminal repeat retrotransposons (LTR-RTs), a major type of class I transposable elements (TEs), are the most abundant repeat element in plants. The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs. However, for non-model species, this remains a challenge. To address this, we developed LTR_Stream for sub-lineage clustering of LTR-RTs in specific or closely related species, providing higher precision than current database-based lineage-level clustering. Using LTR_Stream, we analyzed Retand LTR-RTs in three Papaver species. Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome. For instance, we found autonomous Retand elements could spread among the ancestors of different subgenomes, like retroviruses pandemics, enriching genetic diversity. Additionally, we identified that specific truncated fragments containing transcription factors motifs such as TCP and bZIP may contribute to generation of novel TAD-like boundaries. Notably, our pre- and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization, suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs. We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.

bioinformatics↗

bioRxiv2025

A Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

Recent advances in sequencing technologies have enabled the complete assembly of human genomes from telomere to telomere (T2T), resolving previously inaccessible regions such as centromeres and segmental duplications. Here, we present an updated, higher-quality, haplotype-phased T2T assembly of the Chinese Quartet (T2T-CQ), a family cohort comprising monozygotic twins and their parents, generated using high-coverage ONT ultralong and PacBio HiFi sequencing. The T2T-CQ assembly serves as a crucial reference genome for integrating publicly available multi-omics data and advances the utility of the Quartet reference materials. The T2T-CQ assembly scores highly on multiple metrics of continuity and completeness, with Genome Continuity Inspector (GCI) scores of 77.76 (maternal) and 76.41 (paternal), quality values (QV) > 70, and Clipping Reveals Assembly Quality (CRAQ) scores > 99.6 for both haplotypes, enabling complete annotation of centromeric regions. Within these regions, we identified novel 13-mer higher-order repeat patterns on chromosome 17 which exhibited a monophyletic origin and emerged approximately 230 thousand years ago. Overall, this work establishes an essential genomic resource for the Han Chinese population and advances the development of a T2T pan-Chinese reference genome, which will significantly enable future investigations both into population-specific structural variants and the evolutionary dynamics of centromeres.

genomics↗